TnSeqCorr

• These are correlations of TnSeq responses across 82 experimental conditions.
• LFCs (log2-fold-changes) were computed for each gene in each condition relative to a relevant control condition (e.g. H37Rv grown on 7H9).
• The LFCs were normalized by dividing by the standard deviation for each condition. (so roughly, |LFC|>2 are the outliers, i.e. tails of the distribution)
• Note that essential genes often have LFCs around 0.
• Data for some genes is not available if they have less than 3 TA sites, or the dynamic range of LFCs is less than 2.0 across all conditions. (This is the case for many essential genes.)
• 'leverage' on each plot is a statistical score that indicates how much the regression is influenced by a few outlier points; the traditional threshold is indicated on the plots (3p/n, which is about 0.07 for this dataset), but in practice, cases with leverage > ~0.2 seem to be the least reliable (most misleading) correlation coefficients.

Top 10 genes with highest correlation to Rv3885c/eccE2:

update plot	correlation	link to info on gene
Rv1500/-	(cc=0.6042)	info on Rv1500/-
Rv3153/nuoI	(cc=0.5769)	info on Rv3153/nuoI
Rv2430c/PPE41	(cc=0.5711)	info on Rv2430c/PPE41
Rv3429/PPE59	(cc=0.5608)	info on Rv3429/PPE59
Rv0989c/grcC2	(cc=0.5607)	info on Rv0989c/grcC2
Rv1059/-	(cc=0.5575)	info on Rv1059/-
Rv3151/nuoG	(cc=0.5486)	info on Rv3151/nuoG
Rv0059/-	(cc=0.5436)	info on Rv0059/-
Rv2584c/apt	(cc=0.5426)	info on Rv2584c/apt
Rv0822c/-	(cc=0.5404)	info on Rv0822c/-

Correlation of Rv3885c/eccE2 with Rv0822c/-

Normalized LFCs for Rv3885c/eccE2:
(description and provenance of datasets)

	Rv3885c/eccE2	Rv0822c/-
Fe_supp_jason_reseq	0.44	-0.336
low_pH_jason_reseq	-0.385	-0.756
NO_jason_reseq	-0.533	-0.27
B6_jason_reseq	-0.165	-1.076
MHCII_jason_reseq	0.452	-0.457
Isoniazid02	0.063	0.109
Rifampicin4	-0.079	-0.19
Ethambutol3	0.102	0.764
Meropenem3	0.678	0.317
Vancomycin16	0.114	0.334
Rv2680_day32	0.511	-0.501
H37Rv_KO_MarP	0.243	-0.617
hypoxia_3wks	0.0	0.159
hypoxia_6wks	0.487	0.157
glycerol	0.462	-0.161
cholesterol	-0.15	0.331
AJ	0.133	0.353
Bibs02	0.787	0.144
Bibs02c	0.844	0.502
BL6	1.101	0.743
BL6a	1.492	1.042
BXD01	0.643	0.715
BXD010	0.568	1.18
BXD011	1.032	0.663
BXD03	1.332	1.16
BXD04	0.432	0.707
BXD05	0.935	0.905
BXD06	1.031	1.181
BXD07	1.253	1.02
BXD08	0.896	0.768
BXD09	1.072	1.011
CAST	-0.289	0.536
CCcont	1.222	0.625
DS01	0.986	0.549
DS02	0.993	0.181
DS04	-0.159	0.869
DS0c	1.226	0.528
GP01	0.655	1.013
GP02	1.569	0.996
GP0c	0.559	0.214
NOD	-0.547	0.83
NZO	-0.295	0.763
PWK	1.04	1.06
H37Rv_KO_CtpC	1.193	0.627
H37Rv_KO_CtpD	1.848	1.105
H37Rv_KO_Rv1272	0.98	0.322
H37Rv_KO_SugABC	1.39	0.431
H37Rv_KO_MbtN	-0.544	0.005
Trans05	-0.135	0.975
macrophage_unactivated	-0.224	0.59
IL1	0.0	0.139
Rapamycin	-0.129	0.261
Tcell	0.046	0.678
GMCSF	0.512	0.961
IFNab	0.438	0.532
IFNg	0.144	0.326
IFNg_GMCSF1	0.0	0.16
Rv1432_day32	0.525	0.681
Rv1565c_day32	0.126	-1.72
secA2_input	-0.56	-0.517
delta_Rv3594	-0.823	-0.116
delta_Rv3717	-0.836	-0.316
delta_Rv3811	-0.629	-0.29
delta_Rv0954	-0.506	-0.649
PonA1	-0.157	-0.352
EccD1_KO	0.585	-0.5
EspI_KO	0.143	-0.117
PE35_KO	-0.265	-0.23
PPE68_KO	0.118	-0.784
glycerol2	0.345	-0.175
lignocerate	0.257	-0.524
oleate	0.058	0.007
phosphatidylcholine	0.14	-0.62
acetate	-0.178	-1.034
glucAc	-0.111	-0.789
Rv0950ko	-0.362	-0.335
Rv1096ko	0.087	0.44
Rv3684ko	0.187	0.013
delta_otsA_trehalose	0.833	0.707